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Volume 72,
Issue 6,
2023
Volume 72, Issue 6, 2023
- Microbiome and Microbial Ecology in Health
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Compositional shifts within the denture-associated bacteriome in pneumonia – an analytical cross-sectional study
Introduction. Bacterial pneumonia is a common cause of morbidity and mortality in elderly individuals. While the incidence of edentulism is falling, approximately 19 % of the UK population wear a full or partial removable denture. Despite advances in denture biomaterials, the majority of dentures are fabricated using polymethyl-methacrylate. Growing evidence suggests that colonization of the oral cavity by putative respiratory pathogens predisposes individuals to respiratory infection, by translocation of these microorganisms along the respiratory tract.
Hypothesis/Gap Statement. We hypothesized that denture surfaces provide a susceptible colonization site for putative respiratory pathogens, and thus could increase pneumonia risk in susceptible individuals.
Aim. This study aimed to characterize the bacterial community composition of denture-wearers in respiratory health compared with individuals with a confirmed diagnosis of pneumonia.
Methodology. This was an analytical cross-sectional study, comparing frail elderly individuals without respiratory infection (n=35) to hospitalized patients with pneumonia (n=26). The primary outcome was the relative abundance of putative respiratory pathogens identified by 16S rRNA metataxonomic sequencing, with quantitative PCR used to identified Streptococcus pneumoniae .
Results. There was a statistically significant increase in the overall relative abundance of putative respiratory pathogens (P<0.0001), with a greater than 20-fold increase in the bioburden of these microorganisms. In keeping with these findings, there were significant shifts in bacterial community diversity (Chao index, P=0.0003) and richness (Inverse Simpson index P<0.0001) in the denture-associated microbiota of pneumonia patients compared with control subjects.
Conclusion. Within the limitations of this study, our evidence supports the role of denture acrylic biomaterials as a potential colonization site for putative respiratory pathogens, which may lead to an increased risk of pneumonia in susceptible individuals. These findings support prior observational studies which have found denture-wearers to be at increased risk of respiratory infection. Further research is needed to confirm the sequence of colonization and translocation to examine potential causal relationships.
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Gut bacteria and sex differences in colorectal cancer
Xi Yang, Ping Li, Zhanbo Qu, Jing Zhuang, Yinhang Wu, Wei Wu and Qichun WeiIntroduction. Differences in gut bacteria that are associated with the occurrence and development of colorectal cancer (CRC) exist between sexes, and males have a higher morbidity of CRC.
Gap Statement. Clinical data for the relationship between gut bacteria and sexes in patients with CRC are not available and are needed to support individualized screening and treatment programmes.
Aim. To analyse the relationship between gut bacteria and sexes in patients with CRC.
Methodology. A total of 6 077 samples recruited by Fudan University’s Academy of Brain Artificial Intelligence Science and Technology were included, and the gut bacteria composition mainly shows the top 30 genera. Linear discriminant analysis Effect Size (LEfSe) was used to analyse the differences in gut bacteria. Pearson correlation coefficients were calculated to demonstrate the relationship of discrepant bacteria. CRC risk prediction models were used to rank the importance of valid discrepant bacteria.
Results. Bacteroides, Eubacterium and Faecalibacterium were the top three bacteria in males with CRC, while Bacteroides, Subdoligranulum and Eubacterium were the top three bacteria in females with CRC. The abundance of gut bacteria ( Escherichia , Eubacteriales , Clostridia, etc.) was higher in males with CRC compared with that in females with CRC. In addition, Dorea and Bacteroides were important CRC-related bacteria (P<0.001). Finally, the importance of discrepant bacteria was ranked based on CRC risk prediction models. Blautia, Barnesiella and Anaerostipes were the top three important discrepant bacteria between males with CRC and females with CRC. The value of AUC was 1.0, the sensitivity was 92.0 %, the specificity was 68.4 %, and the accuracy was 83.3 % in the discovery set.
Conclusion. Gut bacteria were correlated with sexes and CRC. It is necessary to consider gender when gut bacteria are used to treat and predict CRC.
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High-throughput quantification of microbial-derived organic acids in mucin-rich samples via reverse phase high performance liquid chromatography
More LessOrganic acids (short chain fatty acids, amino acids, etc.) are common metabolic byproducts of commensal bacteria of the gut and oral cavity in addition to microbiota associated with chronic infections of the airways, skin, and soft tissues. A ubiquitous characteristic of these body sites in which mucus-rich secretions often accumulate in excess, is the presence of mucins; high molecular weight (HMW), glycosylated proteins that decorate the surfaces of non-keratinized epithelia. Owing to their size, mucins complicate quantification of microbial-derived metabolites as these large glycoproteins preclude use of 1D and 2D gel approaches and can obstruct analytical chromatography columns. Standard approaches for quantification of organic acids in mucin-rich samples typically rely on laborious extractions or outsourcing to laboratories specializing in targeted metabolomics. Here we report a high-throughput sample preparation process that reduces mucin abundance and an accompanying isocratic reverse phase high performance liquid chromatography (HPLC) method that enables quantification of microbial-derived organic acids. This approach allows for accurate quantification of compounds of interest (0.01 mM – 100 mM) with minimal sample preparation, a moderate HPLC method run time, and preservation of both guard and analytical column integrity. This approach paves the way for further analyses of microbial-derived metabolites in complex clinical samples.
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Correlation analysis for alterations of intestinal flora in hepatocellular carcinoma patients: combinatorial detection of Coriobacterium, Atopobium, Coprococcus and Veillonella dispar may be a new method for HCC diagnosis
More LessIntroduction. Hepatocellular carcinoma (HCC) is one of the most common malignant tumours in the world. Due to the characteristics of low early diagnosis rate, high malignancy and rapid progression, the majority of diagnosed patients are in the middle or late stage. Accumulating evidence reveals that intestinal flora imbalance will aggravate HCC by disturbing immune regulation, especially interleukin expression. Therefore, intestinal flora-based methods have the potential to be new diagnostic or therapeutic methods for HCC.
Hypothesis. Compositions of intestinal florae were different between HCC patients and healthy people. Further, intestinal florae may alleviate or aggravate HCCs.
Methods. To determine which intestinal florae and interleukin aggravate HCCs, we studied the differences in intestinal florae composition and interleukin (IL) indices between HCC patients and healthy people. A total of 64 HCC patients and 24 healthy people were recruited, and their fresh stool samples and serum samples were collected for 16S rRNA sequencing and metabolite index measurement.
Results. Data showed that 484 operational taxonomic units (OTUs) and 476 OTUs were detected in the HCC and control groups, respectively. From the phylum level to the species level, 5, 6, 10, 15, 23 and 19 colonies showed differential abundance between the HCC group and healthy people. Moreover, interleukin-6 expression and interleukin-10 expression were significantly different between two groups. Of note, differences of Coriobacterium , Atopobium and Coprococcus at genus level and Veillonella dispar at species level in two groups were significantly related to IL-6 and IL-10.
Conclusion. The abundance of intestinal florae in the HCC group was different from the control group. Additionally, combinatorial detection of Coriobacterium , Atopobium and Coprococcus at genus level and V. dispar at species level may be a new method for HCC diagnosis.
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Metatranscriptome analysis of blood in healthy individuals and irritable bowel syndrome patients
Introduction. Although the presence of micro-organisms in the blood of healthy humans is a relatively new concept, there is a growing amount of evidence that blood might have its own microbiome.
Gap Statement. Previous research has targeted the taxonomic composition of the blood microbiome using DNA-based sequencing methods, while little information is known about the presence of microbial transcripts obtained from the blood and their relation to conditions connected with increased gut permeability.
Aim. To detect potentially alive and active micro-organisms and investigate differences in taxonomic composition between healthy people and patients with irritable bowel syndrome (IBS), we used the metatranscriptomics approach.
Methodology. We collected blood samples from 23 IBS patients and 26 volunteers from the general population, and performed RNAseq on the isolated RNA. Reads corresponding to microbial genomes were identified with Kraken 2’s standard plus protozoa and fungi database, and re-estimated at genus level with Bracken 2.7. We looked for trends in the taxonomic composition, making a comparison between the IBS and control groups, accounting for other different factors.
Results. The dominant genera in the blood microbiome were found to be Cutibacterium , Bradyrhizobium , Escherichia , Pseudomonas , Micrococcus , Delftia , Mediterraneibacter , Staphylococcus , Stutzerimonas and Ralstonia . Some of these are typical environmental bacteria and could partially represent contamination. However, analysis of sequences from the negative controls suggested that some genera which are characteristic of the gut microbiome ( Mediterraneibacter , Blautia , Collinsella , Klebsiella , Coprococcus , Dysosmobacter , Anaerostipes , Faecalibacterium , Dorea , Simiaoa , Bifidobacterium , Alistipes, Prevotella, Ruminococcus ) are less likely to be a result of contamination. Differential analysis of microbes between groups showed that some taxa associated with the gut microbiome ( Blautia , Faecalibacterium , Dorea , Bifidobacterium , Clostridium , Christensenella ) are more prevalent in IBS patients compared to the general population. No significant correlations with any other factors were identified.
Conclusion. Our findings support the existence of the blood microbiome and suggest the gut and possibly the oral microbiome as its origin, while the skin microbiome is a possible but less certain source. The blood microbiome is likely influenced by states of increased gut permeability such as IBS.
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Gut microbiota associated with the mitigation effect of synbiotics on adverse events of neoadjuvant chemotherapy in patients with esophageal cancer: A retrospective exploratory study
Introduction. Our synbiotics ( Lacticaseibacillus paracasei strain Shirota, Bifidobacterium breve strain Yakult, and galacto-oligosaccharides: LBG) helps mitigate serious adverse events such as febrile neutropenia (FN) and diarrhoea in oesophageal cancer patients receiving neoadjuvant chemotherapy (NAC). Unfortunately, LBG therapy does not benefit all patients.
Hypothesis/Gap Statement. Identification of the gut microbiota species involved in adverse events during chemotherapy could help predict the onset of adverse events. Identification of the gut microbiota that influence the efficacy of LBG could also help establish a diagnostic method to identify patients who will respond to LBG before the initiation of therapy.
Aim. To identify the gut microbiota involved in adverse events during NAC and that affect the efficacy of LBG therapy.
Methodology. This study was ancillary to a parent randomized controlled trial in which 81 oesophageal cancer patients were recruited and administered either prophylactic antibiotics or LBG combined with enteral nutrition (LBG+EN). The study included 73 of 81 patients from whom faecal samples were collected both before and after NAC. The gut microbiota was analysed using 16S rRNA gene amplicon sequencing and compared based on the degree of NAC-associated adverse events. Furthermore, the association between the counts of identified bacteria and adverse events and the mitigation effect of LBG+EN was also analysed.
Results. The abundance of Anaerostipes hadrus and Bifidobacterium pseudocatenulatum in patients with no FN or only mild diarrhoea was significantly higher (P<0.05) compared to those with FN or severe diarrhoea. Moreover, subgroup analyses of patients receiving LBG+EN showed that the faecal A. hadrus count before NAC was significantly associated with a risk of developing FN (OR, 0.11; 95 % CI, 0.01–0.60, P=0.019). The faecal A. hadrus count after NAC was positively correlated with intestinal concentrations of acetic acid (P=0.0007) and butyric acid (P=0.00005).
Conclusion. Anaerostipes hadrus and B. pseudocatenulatum may be involved in the ameliorating adverse events and can thus be used to identify beforehand patients that would benefit from LBG+EN during NAC. These results also suggest that LBG+EN would be useful in the development of measures to prevent adverse events during NAC.
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- Molecular and Microbial Epidemiology
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Impact of the COVID-19 restrictions on the epidemiology of Cryptosporidium spp. in England and Wales, 2015–2021: a time series analysis
Introduction. In England and Wales, cryptosporidiosis cases peak in spring and autumn, associated with zoonotic/environmental exposures (Cryptosporidium parvum, spring/autumn) and overseas travel/water-based activities (Cryptosporidium hominis, autumn). Coronavirus disease 2019 (COVID-19) restrictions prevented social mixing, overseas travel and access to venues (swimming pools/restaurants) for many months, potentially increasing environmental exposures as people sought alternative countryside activities.
Hypothesis. COVID-19 restrictions reduced incidence of C. hominis cases and potentially increased incidence of C. parvum cases.
Aim. To inform/strengthen surveillance programmes, we investigated the impact of COVID-19 restrictions on the epidemiology of C. hominis and C. parvum cases.
Methodology. Cases were extracted from the Cryptosporidium Reference Unit (CRU) database (1 January 2015 to 31 December 2021). We defined two periods for pre- and post-COVID-19 restrictions implementation, corresponding to before and after the first UK-wide lockdown on 23 March 2020. We conducted a time series analysis, assessing differences in C. parvum and C. hominis incidence, trends and periodicity between these periods.
Results. There were 21 304 cases (C. parvum=12 246; C. hominis=9058). Post-restrictions implementation incidence of C. hominis dropped by 97.5 % (95 % CI: 95.4–98.6 %; P<0.001). The decreasing incidence trend pre-restrictions was not observed post-restrictions implementation due to lack of cases. No periodicity change was observed post-restrictions implementation. There was a strong social gradient; there was a higher proportion of cases in deprived areas. For C. parvum, post-restrictions implementation incidence fell by 49.0 % (95 % CI: 38.4–58.3 %; P<0.001). There was no pre-restrictions incidence trend but an increasing incidence trend post-restrictions implementation. A periodicity change was observed post-restriction implementation, peaking 1 week earlier in spring and 2 weeks later in autumn. The social gradient was the inverse of that for C. hominis. Where recorded, 22 % of C. hominis and 8 % of C. parvum cases had travelled abroad.
Conclusion. C. hominis cases almost entirely ceased post-restrictions implementation, reinforcing that foreign travel seeds infections. C. parvum incidence fell sharply but recovered post-restrictions implementation, consistent with relaxation of restrictions. Future exceedance reporting for C. hominis should exclude the post-restriction implementation period but retain it for C. parvum (except the first 6 weeks post-restrictions implementation). Infection prevention and control advice should be improved for people with gastrointestinal illness (GI) symptoms to ensure hand hygiene and swimming pool avoidance.
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Long-term surveillance of group B Streptococcus strains isolated from infection and colonization in pregnant women and newborns
Introduction. Group B Streptococcus (GBS) remains the leading cause of bacterial neonatal infections worldwide, despite the spread of recommendations on vaginal screening and antibiotic prophylaxis.
Hypothesis/Gap Statement. There is a need to evaluate the potential changes in GBS epidemiology over time following the introduction of such guidelines.
Aim. Our aim was to perform a descriptive analysis of the epidemiological characteristics of GBS by conducting a long-term surveillance of strains isolated between 2000 and 2018, using molecular typing methods.
Methodology. A total of 121 invasive strains, responsible for maternal infections (20 strains), fetal infections (8 strains) and neonatal infections (93 strains), were included in the study, representing all the invasive isolates during the period; in addition, 384 colonization strains isolated from vaginal or newborn samples were randomly selected. The 505 strains were characterized by capsular polysaccharide (CPS) type multiplex PCR assay and the clonal complex (CC) was assigned using a single nucleotide polymorphism PCR assay. Antibiotic susceptibility was also determined.
Results. CPS types III (32.1 % of the strains), Ia (24.6 %) and V (19 %) were the most prevalent. The five main CCs observed were CC1 (26.3 % of the strains), CC17 (22.2 %), CC19 (16.2 %), CC23 (15.8 %) and CC10 (13.9 %). Neonatal invasive GBS diseases were predominantly due to CC17 isolates (46.3 % of the strains), which mainly express CPS type III (87.5 %), with a very high prevalence in late-onset diseases (76.2 %).
Conclusion. Between 2000 and 2018, we observed a decrease in the proportion of CC1 strains, which mainly express CPS type V, and an increase in the proportion of CC23 strains, mainly expressing CPS type Ia. Conversely, there was no significant change in the proportion of strains resistant to macrolides, lincosamides or tetracyclines. The two molecular techniques used in our study provide almost as much information as classical serotyping and multilocus sequence typing, but are quicker, easy to perform, and avoid long sequencing and analysis steps.
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- One Health ‒ Emerging, Zoonotic and Environmental Diseases
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Fish-associated Streptococcus agalactiae ST283: first human cases reported from Malaysia
In South East Asia, Streptococcus agalactiae ST283 causes sepsis in healthy adults. Raw freshwater fish consumption is the only known risk factor. These two case reports are the first from Malaysia. Although they cluster with Singapore ST283, the epidemiology is complicated by the flow of people and fish across borders.
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- Pathogenesis, Virulence and Host Response
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Characterisation of key genotypic and phenotypic traits of clinical cystic fibrosis Staphylococcus aureus isolates
Introduction. One third of people with CF in the UK are co-infected by both Staphylococcus aureus and Pseudomonas aeruginosa . Chronic bacterial infection in CF contributes to the gradual destruction of lung tissue, and eventually respiratory failure in this group.
Gap Statement. The contribution of S. aureus to cystic fibrosis (CF) lung decline in the presence or absence of P. aeruginosa is unclear. Defining the molecular and phenotypic characteristics of a range of S. aureus clinical isolates will help further understand its pathogenic capabilities.
Aim. Our objective was to use molecular and phenotypic tools to characterise twenty-five clinical S. aureus isolates collected from mono- and coinfection with P. aeruginosa from people with CF at the Royal Victoria Infirmary, Newcastle upon Tyne.
Methodology. Genomic DNA was extracted and sequenced. Multilocus sequence typing was used to construct phylogeny from the seven housekeeping genes. A pangenome was calculated using Roary, and cluster of Orthologous groups were assigned using eggNOG-mapper which were used to determine differences within core, accessory, and unique genomes. Characterisation of sequence type, clonal complex, agr and spa types was carried out using PubMLST, eBURST, AgrVATE and spaTyper, respectively. Antibiotic resistance was determined using Kirby-Bauer disc diffusion tests. Phenotypic testing of haemolysis was carried out using ovine red blood cell agar plates and mucoid phenotypes visualised using Congo red agar.
Results. Clinical strains clustered closely based on agr type, sequence type and clonal complex. COG analysis revealed statistically significant enrichment of COG families between core, accessory and unique pangenome groups. The unique genome was significantly enriched for replication, recombination and repair, and defence mechanisms. The presence of known virulence genes and toxins were high within this group, and unique genes were identified in 11 strains. Strains which were isolated from the same patient all surpassed average nucleotide identity thresholds, however, differed in phenotypic traits. Antimicrobial resistance to macrolides was significantly higher in the coinfection group.
Conclusion. There is huge variation in genetic and phenotypic capabilities of S. aureus strains. Further studies on how these may differ in relation to other species in the CF lung may give insight into inter-species interactions.
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Characterization of a Helicobacter pylori strain with high biofilm-forming ability
Introduction. Helicobacter pylori is highly polymorphic, and some strains are much more likely to cause disease than others. Biofilm formation can help bacteria to survive antibiotic treatment, immune attack and other stresses, promoting persistent infection.
Hypothesis/Gap Statement. We hypothesized that H. pylori isolates from patients with more severe H. pylori-associated disease would be better at forming biofilms than isolates from patients with less severe disease.
Aim. We initially aimed to determine whether or not the biofilm-forming ability of H. pylori isolates was associated with disease in the UK-based patients from whom the bacteria were isolated.
Methodology. Biofilm-forming ability of H. pylori isolates was determined using a crystal violet assay on glass coverslips. The complete genome sequence of strain 444A was generated by hybrid assembly of Nanopore MinION and Illumina MiSeq data.
Results. Although we found no associations between biofilm-forming ability of H. pylori and disease severity in patients, we discovered that strain 444A had particularly high biofilm-forming ability. This strain had been isolated from a patient with gastric ulcer disease and moderate to severe scores for H. pylori-induced histopathology. Analysis of the genome of the high biofilm-forming H. pylori strain 444A revealed that it possesses numerous biofilm- and virulence-associated genes and a small cryptic plasmid encoding a type II toxin–antitoxin system.
Conclusion. There is substantial variation in biofilm-forming ability in H. pylori, but this was not significantly associated with disease severity in our study. We identified and characterized an interesting strain with high biofilm-forming ability, including generation and analysis of the complete genome.
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- Prevention, Therapy and Therapeutics
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Effect of dextransucrase antibodies on biofilm formation and certain cariogenic activities in Streptococcus mutans
Introduction. Dextransucrase produced by Streptococcus mutans plays a vital role in the formation of dental caries by synthesizing exopolysaccharides from sucrose, which helps in the attachment of microbes to the tooth surface, causing caries. Exploring antibody production against S. mutans antigens could be an effective method to protect against dental caries.
Hypothesis. Dextransucrase antibodies may help in the prevention of caries formation by inhibiting essential cariogenic factors.
Aims. The aim of this study was to investigate the effects of dextransucrase antibodies on biofilm formation and certain associated cariogenic factors of S. mutans .
Methodology. Dextransucrase was purified from culture of S. mutans . The antisera against the enzyme were raised in rabbits. The effect of dextransucrase antibodies on biofilm formation was studied using scanning electron microscopy, fluorescence microscopy and quantitative real-time polymerase chain reaction. The effects of the antibodies on associated cariogenic factors were examined using established methods. The cross-reactivity of antibodies with human lung, liver, heart, thyroid and kidney tissues was evaluated by immunohistochemistry.
Results. Our findings showed impaired biofilm formation in S. mutans in the presence of dextransucrase antibodies. Genes associated with biofilm formation such as gtfB, gtfC, brpA, relA, Smu.630 and vicK were downregulated (50–97 %) by dextransucrase antibodies in S. mutans . The adherence of S. mutans to glass surface was reduced by 58 % and hydrophobicity was reduced by 55.2 % in the presence of the antibodies compared to the controls. Immunohistochemistry studies revealed no cross-reactivity of human tissues with dextransucrase antibodies.
Conclusions. These findings suggest that antibodies raised against dextransucrase exhibit a profound inhibitory effect on biofilm formation and vital cariogenic factors of S. mutans , which supports the contention that dextransucrase could be a promising antigen to study for its anticariogenic potential.
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Novel neutralizing mouse-human chimeric monoclonal antibodies against the SARS-CoV-2 receptor binding domain
Introduction. Neutralizing antibodies have been widely used for the prophylaxis and treatment of COVID-19.
Hypothesis. The major target for these neutralizing antibodies is the receptor-binding domain (RBD) of the viral spike protein.
Aim. In the present study, we developed and characterized three neutralizing chimeric mouse-human mAbs for potential therapeutic purposes.
Methodology. Light and heavy chain variable region genes of three mouse mAbs (m4E8, m3B6, and m1D1) were amplified and ligated to human Cγ1 and Cκ constant region genes by PCR. After cloning into a dual promoter mammalian expression vector, the final constructs were transiently expressed in DG-44 cells and the purified chimeric antibodies were characterized by ELISA and Western blotting. The neutralizing potency of the chimeric mAbs was determined by three different virus neutralization tests including sVNT, pVNT, and cVNT.
Results. All three recombinant chimeric mAbs display human constant regions and are able to specifically bind to the RBD of SARS-CoV-2 with affinities comparable to the parental mAbs. Western blot analysis showed similar epitope specificity profiles for both the chimeric and the parental mouse mAbs. The results of virus neutralization tests (sVNT, pVNT, and cVNT) indicate that c4E8 had the most potent neutralizing activity with IC50 values of 1.772, 0.009, and 0.01 µg ml−1, respectively. All chimeric and mouse mAbs displayed a similar pattern of reactivity with the spike protein of the SARS-CoV-2 variants of concern (VOC) tested, including alpha, delta, and wild-type.
Conclusion. The chimeric mAbs displayed neutralizing potency similar to the parental mouse mAbs and are potentially valuable tools for disease control.
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Volumes and issues
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Volume 74 (2025)
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Volume 72 (2023 - 2024)
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Volume 71 (2022)
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